Adaptive Message Passing: A General Framework to Mitigate Oversmoothing, Oversquashing, and Underreaching

Long-range interactions are essential for the correct description of complex systems in many scientific fields. The price to pay for including them in the calculations, however, is a dramatic increase in the overall computational costs. Recently, deep graph networks have been employed as efficient, data-driven surrogate models for predicting properties of complex systems represented as graphs. These models rely on a local and iterative message passing strategy that should, in principle, capture long-range information without explicitly modeling the corresponding interactions. In practice, most deep graph networks cannot really model long-range dependencies due to the intrinsic limitations of (synchronous) message passing, namely oversmoothing, oversquashing, and underreaching. This work proposes a general framework that learns to mitigate these limitations: within a variational inference framework, we endow message passing architectures with the ability to freely adapt their depth and filter messages along the way. With theoretical and empirical arguments, we show that this simple strategy better captures long-range interactions, by surpassing the state of the art on five node and graph prediction datasets suited for this problem. Our approach consistently improves the performances of the baselines tested on these tasks. We complement the exposition with qualitative analyses and ablations to get a deeper understanding of the framework's inner workings.

Uncertainty-biased molecular dynamics for learning uniformly accurate interatomic potentials

Efficiently creating a concise but comprehensive data set for training machine-learned interatomic potentials (MLIPs) is an under-explored problem. Active learning (AL), which uses either biased or unbiased molecular dynamics (MD) simulations to generate candidate pools, aims to address this objective. Existing biased and unbiased MD simulations, however, are prone to miss either rare events or extrapolative regions -- areas of the configurational space where unreliable predictions are made. Simultaneously exploring both regions is necessary for developing uniformly accurate MLIPs. In this work, we demonstrate that MD simulations, when biased by the MLIP's energy uncertainty, effectively capture extrapolative regions and rare events without the need to know \textit{a priori} the system's transition temperatures and pressures. Exploiting automatic differentiation, we enhance bias-forces-driven MD simulations by introducing the concept of bias stress. We also employ calibrated ensemble-free uncertainties derived from sketched gradient features to yield MLIPs with similar or better accuracy than ensemble-based uncertainty methods at a lower computational cost. We use the proposed uncertainty-driven AL approach to develop MLIPs for two benchmark systems: alanine dipeptide and MIL-53(Al). Compared to MLIPs trained with conventional MD simulations, MLIPs trained with the proposed data-generation method more accurately represent the relevant configurational space for both atomic systems.

Self-Tuning Hamiltonian Monte Carlo for Accelerated Sampling

The performance of Hamiltonian Monte Carlo crucially depends on its parameters, in particular the integration timestep and the number of integration steps. We present an adaptive general-purpose framework to automatically tune these parameters based on a loss function which promotes the fast exploration of phase-space. For this, we make use of a fully-differentiable set-up and use backpropagation for optimization. An attention-like loss is defined which allows for the gradient driven learning of the distribution of integration steps. We also highlight the importance of jittering for a smooth loss-surface. Our approach is demonstrated for the one-dimensional harmonic oscillator and alanine dipeptide, a small protein common as a test-case for simulation methods. We find a good correspondence between our loss and the autocorrelation times, resulting in well-tuned parameters for Hamiltonian Monte Carlo.

Investigating the Interplay between Features and Structures in Graph Learning

In the past, the dichotomy between homophily and heterophily has inspired research contributions toward a better understanding of Deep Graph Networks' inductive bias. In particular, it was believed that homophily strongly correlates with better node classification predictions of message-passing methods. More recently, however, researchers pointed out that such dichotomy is too simplistic as we can construct node classification tasks where graphs are completely heterophilic but the performances remain high. Most of these works have also proposed new quantitative metrics to understand when a graph structure is useful, which implicitly or explicitly assume the correlation between node features and target labels. Our work empirically investigates what happens when this strong assumption does not hold, by formalising two generative processes for node classification tasks that allow us to build and study ad-hoc problems. To quantitatively measure the influence of the node features on the target labels, we also use a metric we call Feature Informativeness. We construct six synthetic tasks and evaluate the performance of six models, including structure-agnostic ones. Our findings reveal that previously defined metrics are not adequate when we relax the above assumption. Our contribution to the workshop aims at presenting novel research findings that could help advance our understanding of the field.

Modeling Edge Features with Deep Bayesian Graph Networks

We propose an extension of the Contextual Graph Markov Model, a deep and probabilistic machine learning model for graphs, to model the distribution of edge features. Our approach is architectural, as we introduce an additional Bayesian network mapping edge features into discrete states to be used by the original model. In doing so, we are also able to build richer graph representations even in the absence of edge features, which is confirmed by the performance improvements on standard graph classification benchmarks. Moreover, we successfully test our proposal in a graph regression scenario where edge features are of fundamental importance, and we show that the learned edge representation provides substantial performance improvements against the original model on three link prediction tasks. By keeping the computational complexity linear in the number of edges, the proposed model is amenable to large-scale graph processing.

Tractable Probabilistic Graph Representation Learning with Graph-Induced Sum-Product Networks

We introduce Graph-Induced Sum-Product Networks (GSPNs), a new probabilistic framework for graph representation learning that can tractably answer probabilistic queries. Inspired by the computational trees induced by vertices in the context of message-passing neural networks, we build hierarchies of sum-product networks (SPNs) where the parameters of a parent SPN are learnable transformations of the a-posterior mixing probabilities of its children's sum units. Due to weight sharing and the tree-shaped computation graphs of GSPNs, we obtain the efficiency and efficacy of deep graph networks with the additional advantages of a purely probabilistic model. We show the model's competitiveness on scarce supervision scenarios, handling missing data, and graph classification in comparison to popular neural models. We complement the experiments with qualitative analyses on hyper-parameters and the model's ability to answer probabilistic queries.

Bayesian Deep Learning for Graphs

The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an increasing interest in the adaptive processing of graphs, which led to the development of different neural network-based methodologies. In this thesis, we take a different route and develop a Bayesian Deep Learning framework for graph learning. The dissertation begins with a review of the principles over which most of the methods in the field are built, followed by a study on graph classification reproducibility issues. We then proceed to bridge the basic ideas of deep learning for graphs with the Bayesian world, by building our deep architectures in an incremental fashion. This framework allows us to consider graphs with discrete and continuous edge features, producing unsupervised embeddings rich enough to reach the state of the art on several classification tasks. Our approach is also amenable to a Bayesian nonparametric extension that automatizes the choice of almost all model's hyper-parameters. Two real-world applications demonstrate the efficacy of deep learning for graphs. The first concerns the prediction of information-theoretic quantities for molecular simulations with supervised neural models. After that, we exploit our Bayesian models to solve a malware-classification task while being robust to intra-procedural code obfuscation techniques. We conclude the dissertation with an attempt to blend the best of the neural and Bayesian worlds together. The resulting hybrid model is able to predict multimodal distributions conditioned on input graphs, with the consequent ability to model stochasticity and uncertainty better than most works. Overall, we aim to provide a Bayesian perspective into the articulated research field of deep learning for graphs.

Catastrophic Forgetting in Deep Graph Networks: an Introductory Benchmark for Graph Classification

In this work, we study the phenomenon of catastrophic forgetting in the graph representation learning scenario. The primary objective of the analysis is to understand whether classical continual learning techniques for flat and sequential data have a tangible impact on performances when applied to graph data. To do so, we experiment with a structure-agnostic model and a deep graph network in a robust and controlled environment on three different datasets. The benchmark is complemented by an investigation on the effect of structure-preserving regularization techniques on catastrophic forgetting. We find that replay is the most effective strategy in so far, which also benefits the most from the use of regularization. Our findings suggest interesting future research at the intersection of the continual and graph representation learning fields. Finally, we provide researchers with a flexible software framework to reproduce our results and carry out further experiments.

Graph Mixture Density Networks

We introduce the Graph Mixture Density Network, a new family of machine learning models that can fit multimodal output distributions conditioned on arbitrary input graphs. By combining ideas from mixture models and graph representation learning, we address a broad class of challenging regression problems that rely on structured data. Our main contribution is the design and evaluation of our method on large stochastic epidemic simulations conditioned on random graphs. We show that there is a significant improvement in the likelihood of an epidemic outcome when taking into account both multimodality and structure. In addition, we investigate how to \textit{implicitly} retain structural information in node representations by computing the distance between distributions of adjacent nodes, and the technique is tested on two structure reconstruction tasks with very good accuracy. Graph Mixture Density Networks open appealing research opportunities in the study of structure-dependent phenomena that exhibit non-trivial conditional output distributions.

Accelerating the identification of informative reduced representations of proteins with deep learning for graphs

The limits of molecular dynamics (MD) simulations of macromolecules are steadily pushed forward by the relentless developments of computer architectures and algorithms. This explosion in the number and extent (in size and time) of MD trajectories induces the need of automated and transferable methods to rationalise the raw data and make quantitative sense out of them. Recently, an algorithmic approach was developed by some of us to identify the subset of a protein's atoms, or mapping, that enables the most informative description of it. This method relies on the computation, for a given reduced representation, of the associated mapping entropy, that is, a measure of the information loss due to the simplification. Albeit relatively straightforward, this calculation can be time consuming. Here, we describe the implementation of a deep learning approach aimed at accelerating the calculation of the mapping entropy. The method relies on deep graph networks, which provide extreme flexibility in the input format. We show that deep graph networks are accurate and remarkably efficient, with a speedup factor as large as $10^5$ with respect to the algorithmic computation of the mapping entropy. Applications of this method, which entails a great potential in the study of biomolecules when used to reconstruct its mapping entropy landscape, reach much farther than this, being the scheme easily transferable to the computation of arbitrary functions of a molecule's structure.